Notes

Metabolite data was included in the model. No scaling of omics views to unit variance. Fitting was performed with medium convergence and 10 factors. No subsets of view features were selected, so views have a substantial inequality in the number of features (especially metabolites, with only around 30 features).

Variance analysis

Factor weight plots

Factor1

View: 16S

View: virome

View: metabolites

Factor3

View: 16S

View: virome

View: metabolites

Factor4

View: 16S

View: virome

View: metabolites

Feature-feature correlation heatmaps

Factor1

Views: 16S_virome

Views: 16S_metabolites

Views: virome_metabolites

Factor3

Views: 16S_virome

Views: 16S_metabolites

Views: virome_metabolites

Factor4

Views: 16S_virome

Views: 16S_metabolites

Views: virome_metabolites

Factor-metabolite correlation

Panel 1

Panel 2

Feature-feature scatter plots

Factor3

Scatter: Lachnospiraceae_vs_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnoclostridium_vs_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Flavonifractor_vs_VC_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Blautia_vs_VC_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Anaerostipes_vs_VC_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Agathobacter_vs_VC_BAC3_V__5269

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnospiraceae_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnoclostridium_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Flavonifractor_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Blautia_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Anaerostipes_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Agathobacter_vs_VC_27_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnospiraceae_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnoclostridium_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Flavonifractor_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Blautia_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Anaerostipes_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Agathobacter_vs_VC_62_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Factor4

Scatter: Bacteroides_vs_VC_117_5

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Bacteroides_vs_VC_117_2

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Parabacteroides_vs_VC_612_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Parabacteroides_vs_VC_122_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Parabacteroides_vs_VC_241_3

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnospiraceae_UCG-004_vs_VC_611_1

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Scatter: Lachnospiraceae_UCG-004_vs_VC_191_0

Metabolite: Butyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: 2-Methylbutyric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Valeric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Isovaleric acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Propionic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Acetic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Dehydrolithocholic acid

## `geom_smooth()` using formula 'y ~ x'

Metabolite: Desaminotyrosine

## `geom_smooth()` using formula 'y ~ x'

Metabolite: ICA

## `geom_smooth()` using formula 'y ~ x'

Factor-factor scatter plots

Factor1_Factor3

GvHD_pre_post

TRM_pre_post

OS_pre_post

pre_post

GvHD

TRM

OS

Factor4_Factor3

GvHD_pre_post

TRM_pre_post

OS_pre_post

pre_post

GvHD

TRM

OS

Factor1_Factor4

GvHD_pre_post

TRM_pre_post

OS_pre_post

pre_post

GvHD

TRM

OS

Factor boxplots by timepoint

Factor1

Factor3

Factor4

sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS/LAPACK: /misc/software/package/RBioC/libmkl/R-4.1.1_buster_intel-mkl-64bit-2020.1-102_build/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gridExtra_2.3      RColorBrewer_1.1-2 pheatmap_1.0.12    dplyr_1.0.7       
##  [5] tidyr_1.1.4        knitr_1.36         MOFA2_1.4.0        patchwork_1.1.1   
##  [9] stringr_1.4.0      rstatix_0.7.0      corrplot_0.91      ggrepel_0.9.1     
## [13] ggpubr_0.4.0       ggplot2_3.3.5      here_1.0.1         rmarkdown_2.11    
## 
## loaded via a namespace (and not attached):
##  [1] MatrixGenerics_1.6.0 sass_0.4.0           splines_4.1.1       
##  [4] jsonlite_1.7.2       carData_3.0-4        bslib_0.3.1         
##  [7] assertthat_0.2.1     highr_0.9            stats4_4.1.1        
## [10] yaml_2.2.1           pillar_1.6.4         backports_1.3.0     
## [13] lattice_0.20-44      glue_1.5.0           reticulate_1.22     
## [16] digest_0.6.28        ggsignif_0.6.3       colorspace_2.0-2    
## [19] cowplot_1.1.1        htmltools_0.5.2      Matrix_1.3-4        
## [22] plyr_1.8.6           pkgconfig_2.0.3      broom_0.7.10        
## [25] dir.expiry_1.2.0     purrr_0.3.4          scales_1.1.1        
## [28] HDF5Array_1.22.1     Rtsne_0.15           tibble_3.1.6        
## [31] mgcv_1.8-36          farver_2.1.0         generics_0.1.1      
## [34] IRanges_2.28.0       car_3.0-12           ellipsis_0.3.2      
## [37] withr_2.4.2          BiocGenerics_0.40.0  magrittr_2.0.1      
## [40] crayon_1.4.2         evaluate_0.14        fansi_0.5.0         
## [43] nlme_3.1-152         forcats_0.5.1        tools_4.1.1         
## [46] lifecycle_1.0.1      matrixStats_0.61.0   basilisk.utils_1.6.0
## [49] Rhdf5lib_1.14.2      S4Vectors_0.32.2     munsell_0.5.0       
## [52] DelayedArray_0.20.0  compiler_4.1.1       jquerylib_0.1.4     
## [55] rlang_0.4.12         rhdf5_2.36.0         rhdf5filters_1.4.0  
## [58] labeling_0.4.2       basilisk_1.6.0       gtable_0.3.0        
## [61] abind_1.4-5          DBI_1.1.1            reshape2_1.4.4      
## [64] R6_2.5.1             fastmap_1.1.0        uwot_0.1.10         
## [67] utf8_1.2.2           filelock_1.0.2       rprojroot_2.0.2     
## [70] stringi_1.7.5        parallel_4.1.1       Rcpp_1.0.7          
## [73] vctrs_0.3.8          png_0.1-7            tidyselect_1.1.1    
## [76] xfun_0.28